Molecular modeling of A1 and A2A adenosine receptors: comparison of rhodopsin- and beta2-adrenergic-based homology models through the docking studies

Adenosine receptors (ARs) are members of the superfamily of G protein-coupled receptors. The homology models of adenosine A1 and A2A receptors were constructed. The high-resolution X-ray structure of bovine rhodopsin and crystal structure of beta2-adrenergic receptor were used as templates. The binding sites of the A1 and A2A ARs were constructed by using data obtained from mutagenesis experiments as well as docking simulations of the respective AR antagonsists DPCPX and XAC. To compare rhodopsin- and beta2-adrenergic-based models, the binding mode of A1 (KW-3902, LUF-5437) and A2A (KW-6002, ZM-241385) ARs antagonists were also examined. The differences in the binding ability of both models were noted during the study. The beta2-adrenergic-based A2A AR model was much more capable to stabilize the ligand in the binding site cavity than the corresponding rhodopsin-based A2A AR model, however, such differences were not so clear in case of A1 AR models. It was suggested that for the A1 AR it is possible to use the crystal structure of rhodopsin as a template as well as beta2-adrenergic receptor, but for A2A AR, with the now available beta2-adrenergic receptor X-ray structure, docking studies should be avoided on the rhodopsin-based model. However, taking into account that the beta2AR shares about 31% of the residues with the AR in comparison to 21% in case of bRho, we suggest using beta2-adrenergic-based models for the A1 and A2A ARs for further in silico ligand screening also because of their generally better ability to stabilize ligands inside the binding pocket.     

Synthesis of an o-Nitrobenzyl Attached A1 Adenosine Receptor Antagonist,a Prodrug Approach

Abstract

The o-nitrobenzyl group, possessing distinct advantage of being photolabile under mild conditions, was successfully connected to 8-(5,6-epoxynorbornan-2-yl)-1,3-dipropylxanthine (5), a high specific A₁ adenosine receptor antagonist. The resulting compound 4 would have potential use as a prodrug.     

Subunit rotation models activation of serotonin 5-HT<Subscript>3AB</Subscript> receptors by agonists

The N-terminal extracellular regions of heterooligomeric 3AB-type human 5-hydroxytryptamine receptors (5-HT3ABR) were modelled based on the crystal structure of snail acetylcholine binding protein AChBP. Stepwise rotation of subunit A by 5 degrees was performed between -10 degrees and 15 degrees to mimic agonist binding and receptor activation. Anticlockwise rotation reduced the size of the binding cavity in interface AB and reorganised the network of hydrogen bonds along the interface. AB subunit dimers with different rotations were applied for docking of ligands with different efficacies: 5-HT, m-chlorophenylbiguanide, SR 57227, quinolinyl piperazine and lerisetron derivatives. All ligands were docked into the dimer with -10 degrees rotation representing ligand-free, open binding cavities similarly, without pharmacological discrimination. Their ammonium ions were in hydrogen bonding distance to the backbone carbonyl of W183. Anticlockwise rotation and contraction of the binding cavity led to distinctive docking interactions of agonists with E129 and cation-pi interactions of their ammonium ions. Side chains of several further amino acids participating in docking (Y143, Y153, Y234 and E236) are in agreement with the effects of point mutations in the binding loops. Our model postulates that 5-HT binds to W183 in a hydrophobic cleft as well as to E236 in a hydrophilic vestibule. Then it elicits anticlockwise rotation to draw in loop C via pi-cation-pi interactions of its ammonium ion with W183 and Y234. Finally, closure of the binding cavity might end in rebinding of 5-HT to E129 in the hydrophilic vestibule.     

Modelling the Interaction of Catecholamines with the α<Subscript>1A</Subscript> Adrenoceptor Towards a Ligand-induced Receptor Structure

Adrenoceptors are members of the important G protein coupled receptor family for which the detailed mechanism of activation remains unclear. In this study, we have combined docking and molecular dynamics simulations to model the ligand induced effect on an homology derived human α_1A adrenoceptor. Analysis of agonist/α_1A adrenoceptor complex interactions focused on the role of the charged amine group, the aromatic ring, the N-methyl group of adrenaline, the beta hydroxyl group and the catechol meta and para hydroxyl groups of the catecholamines. The most critical interactions for the binding of the agonists are consistent with many earlier reports and our study suggests new residues possibly involved in the agonist-binding site, namely Thr-174 and Cys-176. We further observe a number of structural changes that occur upon agonist binding including a movement of TM-V away from TM-III and a change in the interactions of Asp-123 of the conserved DRY motif. This may cause Arg-124 to move out of the TM helical bundle and change the orientation of residues in IC-II and IC-III, allowing for increased affinity of coupling to the G-protein.     

Alpha7 nicotinic acetylcholine receptor agonists: prediction of their binding affinity through a molecular mechanics Poisson-Boltzmann surface area approach

A group of agonists for the alpha7 neuronal nicotinic acetylcholine receptors (nAChRs) was investigated, and their free energies of binding DeltaG(bind) were calculated by applying the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach. This method, based on molecular dynamics simulations of fully solvated protein-ligand complexes, allowed us to estimate the contribution of both polar and nonpolar terms as well as the entropy to the overall free energy of binding. The calculated results were in a good agreement with the experimentally determined DeltaG(bind) values, thereby pointing to the MM-PBSA protocol as a valuable computational tool for the rational design of specific agents targeting the neuronal alpha7 nAChR subtypes.     

Modelling Drugs and Receptors Using Potentials: Examples in the GPCRs' Domain

Abstract

Shape complementarity, electrostatic and hydrophobic matching, were used to model drugs and receptors. From known experimental data on α_1A/α_2A?adrenergic ligands and α_1A/α_2A?alrenoceptors, a model for the ligand binding sites, based on the structure of bacteriorhodopsin as a template, was proposed and built. Agonists and antagonists have overlapping but different binding sites. Emphasis was given on the role of the disulphide bridge and on the role of the sodium site. The model was extended to other G-protein coupled receptors.     

CCl2(A 1B 1,a3B1)自由基被烷烃类分子猝灭动力学

用放电 LIF实验装置,对CCl4/Ar混合气体放电产生CCl2自由基,再用541.52 nm激光将电子基态CCl2激励到激发态A 1B1(0,4,0)振动能级上,通过检测激发态CCl2时间分辨荧光信号,测得室温下CCl2(A 1B1)被烷烃类分子猝灭的实验结果,用我们提出的三能级模型分析处理实验数据,获得CCl2(A 1B1)态和CCl2(a 3B1)态的碰撞猝灭速率常数kA和ka值.     

氨蒸发诱导法制备纳米结构LiNi1/3Co1/3Mn1/3O2及其作为高功率型锂离子电池正极材料的性能

采用氨蒸发诱导法成功制备出纳米结构LiNi_1/3Co_1/3Mn_1/3O₂正极材料,借助X射线衍射（XRD）分析、扫描电镜（SEM）、透射电镜（TEM）、高分辨率透射电镜（HRTEM）、能量分散谱（EDS）和比表面测试等表征手段及恒电流充放电测试研究了其晶体结构、微观形貌和电化学性能. 研究表明该方法制备出的材料具有良好的α-NaFeO₂层状结构,阳离子混排程度低. 纳米片交错堆积而成核桃仁状形貌,片与片之间形成许多纳米孔,而且纳米片的侧面属于{010}活性面,能够提供较多的锂离子的脱嵌通道. 在室温下及3.0-4.6 V充放电范围内,该材料在电流密度为0.5C、1C、3C、5C和10C时放电比容量分别为172.90、153.95、147.09、142.16 和131.23mAh·g^-1. 说明其具有优异的电化学性能,非常有潜力用于动力汽车等高功率密度锂离子电池中.     

A comparative study of CH4 and CF4 rf discharges using a consistent plasma physics and chemistry simulator

A self-consistent, one-dimensional simulator for the physics and chemistry of radio frequency (rf) plasmas was developed and applied for CH₄ and CF₄. The simulator consists of a fluid model for the discharge physics, a commercial Boltzmann equation solver for calculations of electron energy distribution fuction (EEDF), a generalized plasma chemistry code, and an interface module among the three models. The CH₄ and CF₄ discharges are compared and contrasted: CH₄ plasmas are electropositive, with negative ion densities one order of magnitude less than those of electrons, whereas CF₄ plasmas are electronegative, with ten times more negative ions than electrons. The high-energy tail of tire EEDF in CH₄, lies below both the Druyvensteyn and Maxwell distributions, whereas tire EEDF high-energy tail in CF₄ lies between the two. For CH₄, the chemistry model was applied for four species, namely, CH₄ CH₃ CH₂, and H, whereas for CF₄, five species were examined namely CF₄, CF₃, CF₂, CF, and F The predicted densities and profiles compare favorably with experimental data. Finally, the chemistry results were fedback into the physics model until convergence was obtained.     

Exploring the structural requirements in multiple chemical scaffolds for the selective inhibition of Plasmodium falciparum calcium-dependent protein kinase-1 (PfCDPK-1) by 3D-pharmacophore modelling,and docking studies

Current research on antimalarial protein kinases has provided an opportunity to design kinase-based antimalarial drugs. We have developed a common feature-based pharmacophore model from a set of multiple chemical scaffolds including derivatives of 3,6-imidazopyridazines, pyrazolo[2,3-d]pyrimidines and imidazo[1,5-a]pyrazines, in order to incorporate the maximum structural diversity information in the model for the Plasmodium falciparum calcium-dependent protein kinase-1 (PfCDPK-1) target. The best pharmacophore model (Hypo-1) with the essential features of two hydrogen bond donors (HBD), one hydrophobic aromatic (HYAr) and one ring aromatic (RA) showed the classification accuracies of 86.27%, 78.43% and 100.00% in labelling the training and test set (test set-1 and test set-2) compounds into more active and less active classes. In order to identify the crucial interaction between multiple scaffold ligands and the target protein, we first developed the homology model using a template structure of P. bergheii (PbCDPK1; PDB ID: 3Q5I), and thereafter performed the docking studies. The residues such as Lys85, Phe147, Tyr148, Leu198, Val211, and Asp212 were found to be the most important interacting residues for possessing PfCDPK-1 inhibitory activity.     

Modelling and mutation studies on the histamine H1-receptor agonist binding site reveal different binding modes for H1-agonists: Asp116 (TM3) has a constitutive role in receptor stimulation

Summary A modelling study has been carried out, investigating the binding of histamine (Hist), 2-methylhistamine (2-MeHist) and 2-phenylhistamine (2-PhHist) at two postulated agonistic binding sites on transmembrane domain 5 (TM5) of the histamine H₁-receptor. For this purpose a conformational analysis study was performed on three particular residues of TM5, i.e., Lys²⁰⁰, Thr²⁰³ and Asn²⁰⁷, for which a functional role in binding has been proposed. The most favourable results were obtained for the interaction between Hist and the Lys²⁰⁰/Asn²⁰⁷ pair. Therefore, Lys²⁰⁰ was subsequently mutated and converted to an alanine, resulting in a 50-fold decrease of H₁-receptor stimulation by histamine. Altogether, the data suggest that the Lys²⁰⁰/Asn²⁰⁷ pair is important for activation of the H₁-receptor by histamine. In contrast, analogues of 2-PhHist seem to belong to a distinct subclass of histamine agonists and an alternative mode of binding is proposed in which the 2-phenyl ring binds to the same receptor location as one of the aromatic rings of classical histamine H₁-antagonists. Subsequently, the binding modes of the agonists Hist, 2-MeHist and 2-PhHist and the H₁-antagonist cyproheptadine were evaluated in three different seven--helical models of the H₁-receptor built in homology with bacteriorhodopsin, but using three different alignments. Our findings suggest that the position of the carboxylate group of Asp¹¹⁶ (TM3) within the receptor pocket depends on whether an agonist or an antagonist binds to the protein; a conformational change of this aspartate residue upon agonist binding is expected to play an essential role in receptor stimulation.Abbreviations 2-MeHist 2-methylhistamine - 2-PEA 2-pyridyl-ethylamine - 2-PhHist 2-phenylhistamine - CHO Chinese hamster ovary - E_int interaction energy - E_str strain energy - GES global energy structure - gpH₁R guinea pig H₁-receptor - GPCR G-protein coupled receptor - Hist histamine - N proximal nitrogen - N tele nitrogen - TM transmembrane domain - WT wild type     

Development of a Laser Nephelometric Method for the Quantitation of Human Glycohemoglobins

Abstract

A nephelometric procedure for quantitative measurement of glycohemoglobin (Hb A₁) was developed, evaluated, and compared with the semi-quantitative mini-column chromatographic procedure. Hb A₁ was purified from human red cell hemolystate by Bio-Rex 70 ion-exchange liquid chromatography and was used for standards and immunization. The antisera raised in rabbits showed high cross-reactivities with normal human hemoglobin (Hb A). The latter was separated by mixing 25 μl of patients' hemolystate with 2 ml ion-exchange resin suspension for 15 minutes. One hundred microiters of the supernatant was incubated with 900 μl antiserum (dilution 1:50) for 45 minutes at room temperature. Samples were then read on a laser nephelometer. The sensitivity of the assay was found to be 0.1 mg Hb A₁. The intraassay relative standard deviation (RSD) was 5.6% and the interassay RSD was 6.5%.     

A hydrogen-1, nitrogen-15, and chlorine-35 NMR coordination study of Lu(ClO4)3 and Lu(NO3)3 in aqueous solvent mixtures

A coordination study of Lu(III) has been carried out for the nitrate and perchlorate salts in aqueous mixtures of acetone-d₆ and Freon-12 by¹H,¹⁵N and³⁵Cl NMR spectroscopy. At temperatures lower than –90°C, proton and ligand exchange are slow enough to permit the direct observation of¹H resonance signals for coordinated and free water molecules, leading to an accurate measure of the Lu(III) hydration number. In perchlorate solution, in the absence of inner-shell ion-pairing, Lu(III) exhibits a maximum coordination number of six over the allowable concentration range of study, contrasting markedly with the report of values of six to nine or greater as determined by a similar NMR method. The absence of contact ion-pairing was confirmed by³⁵Cl NMR chemical shift and linewidth measurements. Extensive ion-pairing was observed in the nitrate solutions as reflected by the lower Lu(III) hydration numbers of two to three in these systems, the observation of two coordinated water signals, and¹⁵N NMR signals for two complexes. The¹H and¹⁵N NMR spectra and the hydration number could be accounted for by the presence of (H₂O)₄Lu(NO₃)²⁺ and (H₂O)₂Lu(NO₃) ₂ ¹⁺ .     

Structural stability of the solvated cellulose IIII crystal models: a molecular dynamics study

Molecular dynamics (MD) simulations of cellulose III_I crystal models have been carried out. The crystal models were composed by either 24 or 48 cellooligomers consisting of either 20 or 40 residues and were surrounded by waters in a periodic boundary box. Two base plane types differing in a constituent crystal lattice plane, (0 −1 0) × (0 1 0) and (1 0 0) × (0 1 0), were additionally considered. Among the resulting eight crystal models, an overall structure conversion was observed for the seven models. The final structures had a triclinic-like chain arrangement involving one-quarter staggering chains with respect to its axis. The successive, local transformation involving cooperative bends in cellooligomers was observed during the structure conversion. Only the 48 × 20-mer model having the (0 −1 0) lattice plane retained the original crystal structure throughout a 2.5-ns simulation. The MD simulations with an implicit solvent system and a vacuum system were also performed to asses a solvent effect on the structure conversion.     

Investigation on the isoform selectivity of novel kinesin-like protein 1 (KIF11) inhibitor using chemical feature based pharmacophore,molecular docking,and quantum mechanical studies

Kinesin-like protein (KIF11) is a molecular motor protein that is essential in mitosis. Removal of KIF11 prevents centrosome migration and causes cell arrest in mitosis. KIF11 defects are linked to the disease of microcephaly, lymph edema or mental retardation. The human KIF11 protein has been actively studied for its role in mitosis and its potential as a therapeutic target for cancer treatment. Pharmacophore modeling, molecular docking and density functional theory approaches was employed to reveal the structural, chemical and electronic features essential for the development of small molecule inhibitor for KIF11. Hence we have developed chemical feature based pharmacophore models using Discovery Studio v 2.5 (DS). The best hypothesis (Hypo1) consisting of four chemical features (two hydrogen bond acceptor, one hydrophobic and one ring aromatic) has exhibited high correlation co-efficient of 0.9521, cost difference of 70.63 and low RMS value of 0.9475. This Hypo1 is cross validated by Cat Scramble method; test set and decoy set to prove its robustness, statistical significance and predictability respectively. The well validated Hypo1 was used as 3Dquery to perform virtual screening. The hits obtained from the virtual screening were subjected to various scrupulous drug-like filters such as Lipinski’s rule of five and ADMET properties. Finally, six hit compounds were identified based on the molecular interaction and its electronic properties. Our final lead compound could serve as a powerful tool for the discovery of potent inhibitor as KIF11 agonists.     

高密度非球形和球形LiNi1/3Mn1/3Co1/3O2的合成和性能比较

利用二次干燥法和共沉淀法分别制备出了非球形的Ni_1/3Co_1/3Mn_1/3OOH前驱体和球形Ni_1/3Co_1/3Mn_1/3(OH)₂前驱体, 并分别和LiNO₃混合烧结合成高密度非球形和球形的锂离子正极材料Li(Ni_1/3Co_1/3Mn_1/3)O₂. XPS分析表明, 二次干燥法制备的非球形Ni_1/3Co_1/3Mn_1/3OOH前驱体其过渡金属Ni, Co和Mn的价态分别是＋2, ＋3和＋4, 而共沉淀法制备的球形Ni_1/3Co_1/3Mn_1/3(OH)₂前驱体其各金属价态为＋2; X射线衍射分析表明, 非球形的Ni_1/3Co_1/3Mn_1/3OOH前驱体比球形的前驱体具有较高的活性, 能够在低温下合成出Li(Ni_1/3Co_1/3Mn_1/3)O₂, 而且制备的产物结晶度高, 具有规整的层状α-NaFeO₂结构, 扫描电镜显示制备的非球形产物颗粒均匀, 颗粒间隙小, 振实密度高达2.95 g•cm^－3, 远高于球形的振实密度2.35 g•cm^－3; 充放电实验表明, 由非球形前驱体制备的Li(Ni_1/3Co_1/3Mn_1/3)O₂其充放电性能和循环性能以及体积比容量均高于球形正极材料.     

Nitrite formation in aerated aqueous azide solutions: A radiation chemical study

Gamma radiolysis of oxygenated 1–10 mM azide solutions was carried out at various pH values. In oxygenated 10 mM azide solutions, H₂O₂ and NO ₂ ⁻ were observed as radiolytic products while NH3 was not. The concentration of H₂O₂ reached its maximum level at a dose of 1 kGy, whereas NO ₂ ⁻ yield increased non-linearly beyond 2 kGy in this system. Both in aerated and oxygenated systems, G(NO ₂ ⁻ ) and G(H₂O₂) were found to vary with N ₃ ⁻ concentration. The yield of NO ₂ ⁻ was found to be dependent on both dose rate and pH. On pulse radiolysis, NO ₂ ⁻ was found as a radiolytic product in aerated 1 mM azide solution at pH 6.8. In this system the intermediate generated exhibits absorbance around 250 nm. The overall results obtained during the present study reveal that in presence of both reducing radical (mainly e _aq ⁻ ) and oxygen, N ₃ ⁻ produced an intermediate possibly NH₂O ₂ ^• radical, which is the prime source for NO ₂ ⁻ generation.     

Crystal and Molecular Structure of 1-( p -Tolyl)-4-[4-(N-naphthalimido)butyl]piperazine

An X-ray structure analysis of 1-(p-tolyl)-4-[4-(N-naphthalimido)butyl]piperazine (I) was carried out: a=9.551(3), b=13.775(3), á=8.917(4) , =103.96(3), =101.47(4), =92.60(3)°, V=1110.4(7) ³, Z=2,_calc=1.279 g/cm³, =0.644 mm, space group P 1, 4239 nonzero reflections, R=0.056. The molecule is linear elongated. The p-tolyl and naphthalimide fragments are almost planar, while the piperazine cycle has a chair conformation. The long well-packed molecules form parallel and antiparallel chains with van der Waals interactions between them.     

On the use of ionic liquids as mobile phase additives in high-performance liquid chromatography. A review

The popularity of ionic liquids (ILs) has grown during the last decades in several analytical separation techniques. Consequently, the number of reports devoted to the applications of ILs is still increasing. This review is focused on the use of ILs (mainly imidazolium-based associated to chloride and tetrafluoroborate) as mobile phase additives in high-performance liquid chromatography (HPLC). In this approach, ILs just function as salts, but keep several kinds of intermolecular interactions, which are useful for chromatographic separations. Both cation and anion can be adsorbed on the stationary phase, creating a bilayer. This gives rise to hydrophobic, electrostatic and other specific interactions with the stationary phase and solutes, which modify the retention behaviour and peak shape. This review updates the advances in this field, with emphasis on topics not always deeply considered in the literature, such as the mechanisms of retention, the estimation of the suppressing potency of silanols, modelling and optimisation of the chromatographic performance, and the comparison with other additives traditionally used to avoid the silanol problem.